Differential expression slides, HTML, PDF, Rmd

Gene ID conversion slides, HTML, PDF, Rmd

Exercises

Differential expression using limma, Rmd , HTML

Differential expression using sam, Rmd , HTML

Gene ID conversion using biomaRt, biomaRt.R

Extracting gene coordinates using annotables, grch37_gene_classes_to_BED.R

References

• Original limma paper

Smyth, Gordon K. “Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments.” Statistical Applications in Genetics and Molecular Biology 3 (2004) http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.412.1072&rep=rep1&type=pdf

• limma package https://bioconductor.org/packages/release/bioc/html/limma.html and highly useful manual (chapters 8, 9) https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

• Most current overview of limma philosophy and capabilities

Ritchie, Matthew E., Belinda Phipson, Di Wu, Yifang Hu, Charity W. Law, Wei Shi, and Gordon K. Smyth. “Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies.” Nucleic Acids Research 2015 http://nar.oxfordjournals.org/content/43/7/e47.long

• Original sam paper

Tusher, V. G., R. Tibshirani, and G. Chu. “Significance Analysis of Microarrays Applied to the Ionizing Radiation Response.” PNAS 2001 [http://www.pnas.org/content/98/9/5116.long] (http://www.pnas.org/content/98/9/5116.long)

• samr package https://cran.r-project.org/web/packages/samr/index.html